For me, the best scores has to be the ones that best keeps me going. Also happens to be some of the better scores, in general. While I really, really liked the OST for Red Dead Redemption, my favourite is the one for Silent Hill 2. Akira Yamaoka really did something amazing there.
The one soundtrack that can take me through my full spectrum of emotions and remember every little teeny part of the game, and the periods where I've been playing that.